Review: Saudi Arabian Y-Chromosome diversity...relationship with nearby regions

It has become fashionable within elements of 'western' academia, to shift traditionally African-ascribed markers unit by unit to overseas origins, while very few are open to the possibilities that markers long taken for granted as "Eurasian" could actually be of direct African origin. The drivers for such moves can be a matter of trying to shift the Out Of Africa conception of human origins overseas, on a piece by piece and gradual basis, especially given preexisting scant substantiation to the contrary, or else a matter of not coming to terms with the prospect of recent African ancestry in "non-African" territories, which is determined to tarnish "racial purity" by racist cliques, and/or implicates Africans—particularly "black Africans"—as agents of certain "important" sociocultural turning points or "technological breakthroughs" in human history. In this respect, as a common example among many, haplogroup E—the predominant contemporary Y-DNA phylogeny on the African continent which has not only gained reputation for spilling over the boundaries of Africa in a substantial way, but also tied to "turning points" in human history, like say, the turn to a farming economy during the Neolithic era—has gained elevated interest over the years. This interest has accompanied the effort to shift the origins of the haplogroup from Africa to "Eurasia" via a "Middle Eastern origin" theory by certain parties. An earlier example of this, by Chandrasekar & co. (2007), had been discussed on this site; the example this time around comes from Abu-Amero et al. (2009), which will be the subject of review of this blog entry.

First, a quick look at the study via the abstract:

BACKGROUND:
Human origins and migration models proposing the Horn of Africa as a prehistoric exit route to Asia have stimulated molecular genetic studies in the region using uniparental loci. However, from a Y-chromosome perspective, Saudi Arabia, the largest country of the region, has not yet been surveyed. To address this gap, a sample of 157 Saudi males was analyzed at high resolution using 67 Y-chromosome binary markers. In addition, haplotypic diversity for its most prominent J1-M267 lineage was estimated using a set of 17 Y-specific STR loci.

RESULTS:
Saudi Arabia differentiates from other Arabian Peninsula countries by a higher presence of J2-M172 lineages. It is significantly different from Yemen mainly due to a comparative reduction of sub-Saharan Africa E1-M123 and Levantine J1-M267 male lineages. Around 14% of the Saudi Arabia Y-chromosome pool is typical of African biogeographic ancestry, 17% arrived to the area from the East across Iran, while the remainder 69% could be considered of direct or indirect Levantine ascription. Interestingly, basal E-M96* (n = 2) and J-M304* (n = 3) lineages have been detected, for the first time, in the Arabian Peninsula. Coalescence time for the most prominent J1-M267 haplogroup in Saudi Arabia (11.6 +/- 1.9 ky) is similar to that obtained previously for Yemen (11.3 +/- 2) but significantly older that those estimated for Qatar (7.3 +/- 1.8) and UAE (6.8 +/- 1.5).

CONCLUSION:
The Y-chromosome genetic structure of the Arabian Peninsula seems to be mainly modulated by geography. The data confirm that this area has mainly been a recipient of gene flow from its African and Asian surrounding areas, probably mainly since the last Glacial maximum onwards. Although rare deep rooting lineages for Y-chromosome haplogroups E and J have been detected, the presence of more basal clades supportive of the southern exit route of modern humans to Eurasian, were not found.— Abstract ends.

The language applied by the authors here, i.e. when they write "Interestingly, basal E-M96* (n = 2) and J-M304* (n = 3) lineages have been detected, for the first time, in the Arabian Peninsula.", appears to be a reaction to the question around the paucity of basal E clades in the Arabian plate, as raised here for instance, with regards to the aforementioned Chandrasekar et al. (2007) report. What could possibly be "interesting" about basal E-M96 being detected in the Arabian peninsula? The "interesting" aspect, as it turns out, will be used as a platform for moving the origin of the entire haplogroup E family from Africa to the Arabian peninsula. The authors make this bold move, after having repeatedly treated the haplogroup as "African contribution" in Arabian peninsula gene pools through much of the article.

Close examination of the resolution of the lineages typed for the study, however, reveal that these so-called basal markers are likely nothing more than downstream clades that the authors failed to detect due to the insufficient resolution of their research. A more recent research, by Trombetta et al. (2011), has brought to light several downstream hg E clades which were otherwise previously rendered as "basal" or "undifferentiated" clades. The listing of E1b1* (P2) or say, E1b1a* (M2), all of which are characterized by "*" sign, has been interpreted in some amateur quarters as "basal" clades, and therefore supplying strong evidence for "Eurasian" and against the African origins respectively. One only needs to reference up to date Y-DNA phylogenetic tree, to see that these are more than likely downstream clades that eluded detection by the authors. Several downstream clades of the P2 clade, like the E1b1a sub-phylogeny for example, had not been the subject of testing. Likewise, the authors' aforementioned "basal" E-M96* clade(s) could very well be a downstream E1b marker that failed detection for all we know, since the P177 mutation was not the subject of the analysis, just as it could well have been a rare downstream E1 clade, whose characteristic P147 was not the subject of the analysis either. These newly identified mutations however, came to the fore from the DNA sequencing of African samples.

Astonishingly, the authors seemed to have overlooked the fact that the Arabian plate has also been a recipient of deep-root clades that are otherwise generally restricted to Africa—namely, hg A and hg B. It is no accident that these clades are found in the Arabian plate, alongside hg E clades. Conventional wisdom would intuit that they are there, just like hg E, precisely because Africans brought them there after the major Out Of Africa migrations that led to the population of "Eurasia", likely from the early Holocene onwards. The presence of these deep-root clades in the Arabian plate argues against the idea of hg E clades—serving as markers of recent African ancestry—being anomalous in some fashion or another, however seemingly rare they may appear on first encounter. Noteworthy, is that despite this desire to place the origins of a major African haplogroup overseas, the authors do seem to have come to terms with a direct African origin for the E1b1b1c (aka E3b3/E-M123), which could very well have reached the Arabian plate directly from the African Horn, and/or through the Egyptian corridor, as argued on this site 2 years ago. Like maintained here, they too have observed greater internal diversity of east African M123 clades vs. those in the Arabian plate. They make this acknowledgment, on the understanding that E-M123 clades had been detected in greater frequencies in the south Arabian countries (Yemen and Oman) than those of the northern parts of the Arabian plate.

One thing refreshing coming from the authors, unlike many previous occasions in 'western' journals, is their apparent comfort in reporting the possibility that many of the "sub-Saharan" ancestry in the Arabian peninsula comes from human movements preceding the slave trade of the common era. They report that, unlike the reporting from previous journals, namely the Richards et al. (2003): Extensive female-mediated gene flow from sub-Saharan Africa into near eastern Arab populations for example, their findings does not indicate a "strong sexual bias" in the "sub-Saharan" male vs. female contribution into the Arabian gene pool; they note:

Without dismissing the role mediated by slavery, the geographical distribution of these sub-Saharan African lineages in the Arabian Peninsula seems to indicate a prehistoric entrance of a noticeable portion of these lineages that participated in the building of the primitive Arabian population.

Having said that, it's from this point on that the authors start delving into dubious territory, revolving around the origin of the entire E haplogroup. To be specific, the authors treat YAP+ (hg DE) as a molecular ancestor that emerged in the Levant or the Arabian Peninsula before heading to Africa and giving rise to hg E, in the northeastern part of the continent. Mind you, the authors do not base this on any actual detection of a basal ("undifferentiated") YAP+ clade in the Levant or the Arabian peninsula, but rather, on the predication that some 2 "undifferentiated" hg E-M96* clades had been found in their Saudi Arabian samples (sample size 157), and remarkably, represented by what appears to be some 55 individuals out of 916 Lebanese individuals. Given this number, as noted above, it will not be surprising to see these clades turn out to be undetected downstream clades not tested, given the insufficient resolution of the DNA sequencing. The authors themselves openly admit to this:

However, as the authors did not type more markers derived within the E-M96 background such as P147, P177, P2, P75 or M329, more comprehensive phylogenetic resolution of YAP derived Ychromosomes in the Middle East and North and East Africa are necessary to explore the topic further.

It goes without saying, with very little doubt, that hg E super-haplogroup is by far at the pinnacle of its diversity in Africa than anywhere. One has to wonder how a purported homeland of YAP+ in the Arabian plate had managed to stay visibly stunted in its subsequent growth and evolutionary trajectory, while the supposed recipient territories—namely Africa and east Asia—of this clade had managed to acquire this feature.

E clades from the entire Arabian plate all the way to Europe are all derivatives of preexisting African clades. There are no basal branches of hg E that are particularly unique to either of these territories, as the case apparently is in its traditional homeland, Africa. Yet, there is a downstream YAP+ branch that is unique/restricted to eastern Asia, as reflected by the D clade. By the same token—naturally, "undifferentiated" DE-YAP chromosomes had only ever been reported for these same two territories, with the lion's share unsurprisingly going to continental Africa. Going by the authors themselves, the argument goes that hg E would have emerged on the African continent, which then implies that the E-M96* clades that they are using as a platform to put forward an Arabian plate origin for the entire YAP+ family, themselves come from an African origin. To quote the authors:

One DE-YAP* ancestor would have spread to Asia and evolved to haplogroup D while another DE-YAP* returned to northeast Africa and evolved into hg E...to be followed later on by,...

Within this frame [proposed "back-migration" theory for YAP+], it should be expected that E-M96* [aforementioned basal clades] types appear in Africa although its presence in the Arabian Peninsula instead Eastern Africa would not compromise the last proposed model. It could be suggested that these E-M96 Saudi lineages have a sub-Saharan Africa ancestry. 

In short, it is rather odd to posit a non-African origin of YAP+ (aka DE) on the basis of the presence of basal E-M96* clades, which themselves are ultimately determined to be of African origin, in a region where the required basal clades of YAP+ (xE-M96) are absent! Whereas, a number of basal YAP+ (xE-M96) have been reported for African samples, the bulk of which pertain to samples from western Africa as opposed to eastern Africa—meaning, there is no need to seek the ancestor of hg E elsewhere, because all the relevant clades necessary to give rise to this haplogroup are already present in Africa. The authors themselves acknowledge this:

It is noteworthy that DE-YAP* has been detected at low frequency in Africa [37].

As a matter of fact, it has been detected in by far the highest frequency in Africa than anywhere, with at least some 8 cases or so ever reported. Compare that to the 0 case in the Arabian plate, where the authors would nonetheless, like to convince their readers to buy as the likely place of origin. The authors place the likely emerging point for haplogroup E within Africa in northeastern Africa, as it agrees with their preference for a Sinai "exit of modern humans", i.e. out of Africa and into the Levant, where the presumed rise of YAP+ would have occurred, and then made its way to mainland Africa on one hand, and onto east Asia on the other,  as opposed to a "southern exit of modern humans across the Srait of Bab el Mandab". However, that proposal has an uphill battle to fight, since it is general understanding that much of hg E's basal clades are concentrated in "sub-Saharan" Africa, particularly eastern Africa. This suggests a deeply entrenched "southern" origin for hg E, which strongly impairs a Levantine or north Arabian plate YAP+ origin scenario. The authors attempt to buttress this by trying to tie the would-be movement of basic YAP+ markers with the movement of certain mtDNA:

this hypothesis has its mtDNA counterpart as it is well documented that, in the Palaeolithic, at least three clades (X1, U6, M1) derived respectively from the three main Eurasian macrohaplogroups (N, R, M) came back to North Africa from Asia [38-42].

The clades above involve the usual suspects, i.e. U6 and M1, that "back-migration" diffusionist theorists love to use, presumably to argue for Asia-to-Africa movements of humans. It should be noted that all these mtDNA markers the authors name here happen to be African-specific clades. Hg X1 is determined to be "north African and east African-specific" [see Kivisild et al. 2004], while U6 happens to be an autochthonous west Saharan or northwest African clade, whose immediate molecular ancestor remains elusive. The African M1 has no phylogenetic ancestor from Asia, nor is it established that haplogroup M as whole is even Asian in origin to begin with. On the contrary, plenty of candidates exist on the African continent who could well serve as molecular ancestors of hg M as a whole, not just M1. The authors seem to either dismiss or downplay these fine points and attribute "ownership" of these clades to "Eurasia", which they then take for granted as an incontestable truth.

Aside from defending the aforementioned Sinai-to-Levantine route for the dispersal of YAP+ and CF-P143 clades, one might get the impression that the authors had an additional incentive to want to work out an Arabian plate origin for YAP+, and the following could provide clues as to what that might be: 

It could be suggested that these E-M96 Saudi lineages have a sub-Saharan Africa ancestry. However, at least for one of them, all their known male ancestors belong to a big Shammar Arab tribe that ruled much of central and northern Arabia from Riyadh to the frontiers of Syria and northern Iraq. In addition, it might be present in Lebanon [18]. However, as the authors did not type more markers derived within the E-M96 background.

A case can be made that a possible motive exists for safeguarding "revered" ancestors against any "exotic" origin other than that of the Arabian plate. In other words, a desire exists to have these "important" male figures and their "big Shammar" tribe to be "as genuinely Arabian as any other indigenous Arabian". Accordingly, consciously or subconsciously, a "sub-Saharan origin" of these "male ancestors" and their so-called big tribe could be perceived as "taking away" from a genuinely Arabian heritage; that is to say, elements within the Arabian communities could be in danger of having a "false sense of pride" in a social element that is considered highly "desirable" and a source of social pride, which they would want to be a part of but which would otherwise not really be truly "Arabian". Under such a circumstance, conversely, the "important" male ancestors and their tribe would begrudgingly signify the legacy of "African contribution to the Arabian plate" rather than a "locally-sourced symbol of pride". This sort of thing noticeably plays in discussions revolving around ancient Greece for example, wherein Eurocentric elements disavow of any "sub-Saharan" ancestry, as it is perceived as making "Greeks less European" and rendering "Greek legacy" less a matter of locally-sourced "European" symbol of pride, and more a signifier of "African legacy", or "Negro legacy" as some Eurocentrists would prefer to call it. This often results in campaigns to "de-Africanize" ancestry that is otherwise traditionally determined to be "African", usually involving the desire to remove origins of African markers as far away from "sub-Saharan" Africa as possible, since Eurocentrism has essentially turned "sub-Saharan" Africa into a big "Bantustan" of some sort—i.e. the  acceptable "geographical confines" of the "Negro". Hence, it is no accident that coastal north Africa is generally cordoned off from the rest of Africa, usually under the pretext of the Saharan desert, which is treated as a "barrier" in defiance of history to the contrary, while "sub-Saharan" east Africa is rarely treated as though it is part of "sub-Saharan Africa", and instead, often lumped in with "northeastern" Africa. In clear contradiction, latitudinally equivalent territories in western Africa are all too often resolutely treated as "sub-Saharan Africa".

With all this ideological manipulation of African geography, North Africa then turns into a "domain of caucasians". "western" imperialism has had a pivotal role in giving life to these ideological manipulations, whether it's in 'western' nations or overseas, and has gotten to the point, whereby it has even become a matter of government policy in the USA to treat North Africa as "caucasian territory" for census gathering purposes—for example, no matter how ridiculous it comes across to the very people from these locations. Elements within academia are even dismayed by the prospect of Out Of Africa origins of humanity and have been actively campaigning to change that, despite the uphill battle ahead of them; here is Africa "stealing the show" from Europe, which is after all treated as the center of the universe—from the Eurocentric world viewpoint—and should be the spotlight of the world. It is against this ideological background that the "Euro" of "Europe" has to always be emphasized in unnecessary geopolitical constructs like "Eurasia" and "Europe", which could both be effectively placed under the umbrella of Asia in daily discourse, and it is in this climate, that elements within academia are prepared to constrict the acceptable African "boundary" as much as possible in the genetic landscape, while expanding what is determined to be not African to the extent possible, where it becomes almost inconceivable to raise the prospect that elements of "Eurasian" markers—whose integrity is ardently defended—could actually be of direct African origin, while traditional African markers on the other hand, can conceivably be turned into "Eurasian" markers.

*Be on the lookout for possible future updates.
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*References:

—Abu-Amero et al. (2009), Saudi Arabian Y-Chromosome diversity and its relationship with nearby regions.

—Kivisild et al. (2004), Ethiopian Mitochondrial DNA Heritage: Tracking Gene Flow Across and Around the Gate of Tears.

—Richards et al. (2003), Extensive female-mediated gene flow from sub-Saharan Africa into near eastern Arab populations.

—Chandrasekar et al. (2007), YAP insertion signature in South Asia.

—Trombetta et al.(2011), A New Topology of the Human Y Chromosome Haplogroup E1b1 (E-P2) Revealed through the Use of Newly Characterized Binary Polymorphisms.

Supplementary reading:

DE* as "Last Refuge" of Sects so psychologically troubled by African Ancestry?

E-M34: Designation as "African" presents a Dilemma? 

Following Trails of the Cro-Magnon - II 

Summarizing clade M1